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Platform Design Info for Affymetrix miRNA-3_0.
Determining the sample size for adequate power to detect statistical significance is a crucial step at the design stage for high-throughput experiments. Even though a number of methods and tools are available for sample size calculation for microarray and RNA-seq in the context of differential expression (DE), this topic in the field of single-cell RNA sequencing is understudied. Moreover, the unique data characteristics present in scRNA-seq such as sparsity and heterogeneity increase the challenge. We propose POWSC, a simulation-based method, to provide power evaluation and sample size recommendation for single-cell RNA sequencing DE analysis. POWSC consists of a data simulator that creates realistic expression data, and a power assessor that provides a comprehensive evaluation and visualization of the power and sample size relationship.
Platform Design Info for Affymetrix GenomeWideSNP_5.
Platform Design Info for The Manufacturer's Name wheat.
Platform Design Info for Affymetrix RJpGene-1_1-st.
Pviz adapts the Gviz package for protein sequences and data.
Platform Design Info for The Manufacturer's Name Rat230_2.
The Parallel Mixed Model (PMM) approach is suitable for hit selection and cross-comparison of RNAi screens generated in experiments that are performed in parallel under several conditions. For example, we could think of the measurements or readouts from cells under RNAi knock-down, which are infected with several pathogens or which are grown from different cell lines.
Platform Design Info for Affymetrix CynGene-1_1-st.
Platform Design Info for NimbleGen 2006-07-18_mm8_refseq_promoter.
Platform Design Info for Affymetrix MarGene-1_1-st.
Platform Design Info for Affymetrix CanGene-1_0-st.
This package provides a simple framework to facilitate the comparison of pipelines involving various steps and parameters. The `pipelineDefinition` class represents pipelines as, minimally, a set of functions consecutively executed on the output of the previous one, and optionally accompanied by step-wise evaluation and aggregation functions. Given such an object, a set of alternative parameters/methods, and benchmark datasets, the `runPipeline` function then proceeds through all combinations arguments, avoiding recomputing the same step twice and compiling evaluations on the fly to avoid storing potentially large intermediate data.
Platform Design Info for The Manufacturer's Name HG-U133B.
Platform Design Info for Affymetrix RaGene-2_0-st.
Platform Design Info for Affymetrix RaEx-1_0-st-v1.
PWMEnrich pre-compiled background objects for H. sapiens (human) and MotifDb H. sapiens motifs.
An automated pipeline for the detection, integration and reporting of predefined features across a large number of mass spectrometry data files. It enables the real time annotation of multiple compounds in a single file, or the parallel annotation of multiple compounds in multiple files. A graphical user interface as well as command line functions will assist in assessing the quality of annotation and update fitting parameters until a satisfactory result is obtained.
Platform Design Info for Affymetrix RUSGene-1_0-st.
This package provides support for parallelized estimation of GLMs/GEEs, catering for dispersed data.
Platform Design Info for Affymetrix RCnGene-1_0-st.
PartheenMetaData http://swegene.onk.lu.se Annotation Data (PartheenMetaData) assembled using data from public repositories.
This package performs tests for paired high-throughput data.
Platform Design Info for The Manufacturer's Name MG_U74C.